From transmission to evolution: low pathogenic avian influenza (LPAI) H9N2 evolving under poultry vaccination

Summary

The current pandemic reminds us of the shadow of flu caused by avian influenza viruses, which keep circulating and cause outbreaks all over the world. There are two problems with avian influenza viruses (AIVs) that cause flu in poultry: pathogenicity in poultry and possible effects on human health. The high pathogenic avian influenza viruses (HPAIVs) threaten public health directly by high human mortality, and the low pathogenic avian influenza viruses (LPAIVs) play an important role in influenza virus evolution. Due to the mild disease and low death rate, LPAIVs remain circulating in poultry populations, thereby providing a platform and time for the emergence of strains with high transmission, cross host-transmission properties or higher human pathogenicity. More and more human infections, caused by avian influenza virus directly from birds further increase our concerns. The H9N2 subtype LPAIV has attracted attention for its wide range spread in many bird species, as well as for the fact that it has become endemic in commercial poultry in many areas, affecting poultry productivity. As a prevention method, vaccination against the H9N2 subtype virus in poultry was promoted in several countries. However, the persistence of this virus in poultry after vaccination has been reported and it was suggested that the inactivated-virus vaccine might not stop the transmission, but rather trigger the antigenic drift of the virus in poultry. In this thesis, experiments were performed to analyse the effect of the inactivated-virus vaccine on stopping the transmission of H9N2 subtype virus in poultry. In Chapter 2, I showed that the estimated reproduction ratio of H9N2 subtype virus in non-vaccinated and vaccinated chicken was above 1, suggesting that the inactivated-virus vaccine against the H9N2 subtype virus cannot stop the transmission of the homologous virus strain in vaccinated chicken. In Chapter 3, phylogenetic and antigenic analyses of H9N2 subtype virus strains isolated from field markets during 2013-2018 in south China, discovered that a new antigenic group has emerged after 2013. The currently isolated virus strains show a higher number of mutations than the average level observed before, resulting in larger antigenic distances from the vaccine strain. In Chapter 4, I observed evolutionary changes of H9N2 subtype virus strains under continuous selective pressure in different hosts. I also identified changes related to potential antigenic drift events in viruses passaged under antiserum pressure. Then in Chapter 5, I discovered the effects of the PB1 gene from the avian H9N2 strain in the reassortment with a human strain. Corresponding genetic changes were observed in the progeny viruses under selective pressure. Together, this thesis provided experimental and statistical evidence to the assumption that the inactivated virus vaccine cannot stop the transmission of H9N2 subtype LPAIV in a vaccinated chicken population. The H9N2 subtype virus could evolve as a consequence of continuing transmission under selective pressure from the vaccination, and this was observed in the field and in laboratory simulations. In addition, reassortment events involving the PB1 gene of H9N2 subtype virus may drive the emergence of novel reassortant viruses during this ongoing circulation. Based on these findings, it becomes clear that continuous surveillance for LPAIVs in vaccinated poultry is required during and after outbreaks. Monitoring for reassortment variants between LPAIV and human-adapted virus strains deserves more attention for pandemic preparedness.